b-sheets, describe
Parallel, anti-parallel, mixed
Relatively extended conformation
ϕ (phi) and ψ (psi) near (-120, +120) parallel (STAGGER)
ϕ (phi) and ψ (psi) near (-140, +140), antiparallel
sheets formed by H-bonds between strands
Strands may be separated within primary stricture, or come from different peptides
Individual strands in a beta sheet do not necessarily
follow each other within the primary sequence.
b-sheets are not planar, but typically twist into
saddle shapes or barrels
Beta turns are part of irregular secondary structure. It is characterized by
backbone H-bond (C=O of residue 1 to N-H of residue 4)
180 change in direction of polypeptide (can be used to connect antiparallel B strands)
What amino acids are found in beta turns?
proline and glycine
a beta turn is a short stretch of 4 aa
it makes the polypeptide chain reverse direction (180)
the backbone has to bend very sharply - only certain aa can handle that bend
proline - forces a turn (rigid cyclic side chain, locks the phi angle, induces a kink or bend in the chain)
glycine - allows flexibility (no side chiain, maximum conformational freedom, can adopt unusal phi and psi angles that other aa cant)
Number of types characterized by combinations of ϕ (phi) and ψ (psi) angles, most common are
(in beta turns, they can turn into different types based on phi and psi angles of two central residues in the turn)
(several beta turn types have been identified (type I, II, I’, II’, III))
types I and II
type 1: no extreme steric clashes, often has proline at i+1
type 2: second most common, req very tight angle at i+2, glycine often about there bc other amino acids are too bulky
beta turns are common in what proteins?
What type of beta turns have glycine as the 3rd residue?
globular
type II (only gly can adopt the necessary geometry (80, 0) at position i+2 (3rd position) for type II turns
What is propensity?
How likely an amino acid is to adopt a particular structure or behavior
What amino acids favour the alpha helical conformation? Which 3 have the highest propensity for alpha helix formation?
MALEK
met, ala, leu, glu, lys
ala glu met
What amino acids have the lowest propensities in alpha helix formation?
gly and proline
Tertiary structures are determined by
amino acid sequence and the environment in which the protein is found
soluble proteins generally require an aqueous environment to fold properly
membrane protein structures will typically only form properly in the presence of membrane
What forces are critical in determining tertiary structures?
non-covalent forces (hydrophobic effect, van der waals interactions, H-bonds, ionic interactions)
The native conformation is the low energy functional state. The change in G for folding is typically near −100 kJ/mol. There may be more than one stable, functional state, caused by:
binding of ligands (in some cases, such as allostery)
flexible portions of proteins
breathing - kinetic motions of atoms in proteins
The 3D structure of proteins exist in one or a few stable structural forms, such as
secondary structure
supersecondary structures (motifs, domains)
tertiary structures
quaternary structures
What are some methods for determining protein structures?
general characteristics of secondary structure (circular dichroism)
detailed atomic information (X-ray crystallography, protein NMR)
What is circular dichroism?
spectroscopic technique that depends on differential absorption of left and right circularly polarized light
alpha helices, beta sheets, and random coil, irreg structures al have characteristic CD spectra
What is circular dichroism useful in?
denaturation/renaturation experiments
What is X-ray cystallography?
protein prep are used to grow crystals
requires very pure samples
crystals exposed to X rays
info about electron density
What is X-ray diffraction?
crystal is used to generate a diffraction pattern
data from pattern used to calculate 3D electron density map
regions of greatest electron density reveal the location of atomic nuclei
What are the pros and cons of X-ray crystallography?
pros: highly detailed structures, rapid solutions, useful for large proteins/complexes
cons: requires crystal growth, crystals must diffract, structures are static, cannot see hydrogens
What is 2D NMR?
off diagonal peaks are NOE signals generated by close range interactions of protons
combines, these provide info about 3D structure of protein
What is protein NMR?
magnetic coupling provides info about distances between atoms (distance restraints)
combined with ideal geometry info
provides a range of solutions which reflect both motion (dynamics) and error
How can you determine is something was found by NMR
core very well defined
multiple lines represent a family of structures consistent with the distance constraints in NMR data
areas that are less clearly defined may be in motion or have only a few distances determined
What are the pros and cons of protein NMR?
pros: dynamic info, proteins in solution
cons: difficult for large macromolecules, synth of peptides with isotopes can be expensive and time consuming
